hello, I have human gene HR, for which i want to find orthologous protein sequence by using BLAST p bidirectional best hit approach. can i perform this bidirectional blast at ensembl or NCBI data base and How? kindly guide me.
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sayyarsehrish •
Yes, that should be possible online with the NCBI blast interface. Take human protein as input, do blast, get the best hit and use that one to blast again back to human proteins (is a subset available on NCBI blast).
On the other hand, if this is not a school assignment you will likely be better of querying this gene on Ensembl and get the ortholgos from that resource
thanks, I am very beginner at these analysis. I want to perform this blast for article.
I see, but the point remains: much more experienced people have done this exercise for you already (and likely much more thorough than with only RBH analysis) so why do it again?
Go to ensembl (or NCBI homologous DB as GenoMax points out) and simply select the homologs/orthologs
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Not in an automated fashion. You will have to do the searches manually.
You can find pre-computed orthologs in NCBI Homologene database. e.g. Human HRas